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Oligonucleotide Synthesis

Methods and Applications

  • Book
  • © 2005

Overview

Editors:
  1. Piet Herdewijn

    1. Rega Institute, Medicinal Chemistry Lab, Katholieke Universiteit Leuven, Leuven, Belgium

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Part of the book series: Methods in Molecular Biology (MIMB, volume 288)

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About this book

A collection of powerful new techniques for oligonucleotide synthesis and for the use of modified oligonucleotides in biotechnology. Among the protocol highlights are a novel two-step process that yields a high purity, less costly, DNA, the synthesis of phosphorothioates using new sulfur transfer agents, the synthesis of LNA, peptide conjugation methods to improve cellular delivery and cell-specific targeting, and triple helix formation. The applications include using molecular beacons to monitor the PCR amplification process, nuclease footprinting to study the sequence-selective binding of small molecules of DNA, nucleic acid libraries, and the use of small interference RNA (siRNA) as an inhibitor of gene expression.

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Table of contents (25 protocols)

  1. Front Matter

    Pages i-xvi
    Download chapter PDF

  2. Synthesis of DNA Using a New Two-Step Cycle

    • Douglas J. Dellinger, Jason R. Betley, Tadeusz K. Wyrzykiewicz, Marvin H. Caruthers
    Pages 1-16

  3. RNA Synthesis Using 2′-O-(Tert-Butyldimethylsilyl) Protection

    • Brian S. Sproat
    Pages 17-31

  4. RNA Oligonucleotide Synthesis Via 5′-Silyl-2′-Orthoester Chemistry

    • Stephanie A. Hartsel, David E. Kitchen, Stephen A. Scaringe, William S. Marshall
    Pages 33-49

  5. Dimethylthiarum Disulfide

    • Zhiwei Wang, Quanlai Song, Yogesh S. Sanghvi
    Pages 51-63

  6. Assay for Evaluating Ribonuclease H-Mediated Degradation of RNA-Antisense Oligonucleotide Duplexes

    • Annie Galarneau, Kyung-Lyum Min, Maria M. Mangos, Masad J. Damha
    Pages 65-80

  7. Di- and Oligonucleotide Synthesis Using H-Phosphonate Chemistry

    • Jacek Stawinski, Roger Ströberg
    Pages 81-100

  8. Solid-Phase Synthesis of Circular Oligonucleotides

    • Enrique Pedroso, Nuria Escaja, Miriam Frieden, Anna Grandas
    Pages 101-125

  9. Locked Nucleic Acid Synthesis

    • Henrik M. Pfundheller, Anders M. Sørensen, Christian Lomholt, Anders M. Johansen, Troels Koch, Jesper Wengel
    Pages 127-145

  10. Synthesis of DNA Mimics Representing HypNA-pPNA Hetero-Oligomers

    • Vladimir A. Efimov, Oksana G. Chakhmakhcheva
    Pages 147-163

  11. Base-Modified Oligonucleotides With Increased Duplex Stability

    • Frank Seela, Yang He, Junlin He, Georg Becher, Rita Kröschel, Matthias Zulauf et al.
    Pages 165-186

  12. Introduction of Hypermodified Nucleotides in RNA

    • Darrell R. Davis, Ashok C. Bajji
    Pages 187-204

  13. Chemical Methods for Peptide-Oligonucleotide Conjugate Synthesis

    • Dmitry A. Stetsenko, Michael J. Gait
    Pages 205-224

  14. Biotin-Labeled Oligonucleotides With Extraordinarily Long Tethering Arms

    • A. Michael Morocho, Valeri Karamyshev, Olga Shcherbinina, Nikolai Polushin
    Pages 225-240

  15. Universal Labeling Chemistry for Nucleic Acid Detection on DNA Chips

    • Ali Laayoun, Eloy Bernal-Méndez, Isabelle Sothier, Mitsuharu Kotera, Alain Troesch
    Pages 241-250

  16. Postsynthetic Functionalization of Triple Helix-Forming Oligonucleotides

    • Alexandre S. Boutorine, Jian-Sheng Sun
    Pages 251-260

  17. Fluorescence-Based On-Line Detection as an Analytical Tool in RNA Electrophoresis

    • Ute Scheffer, Michael Göbel
    Pages 261-272

  18. Design and Optimization of Molecular Beacon Real-Time Polymerase Chain Reaction Assays

    • Jacqueline A. M. Vet, Salvatore A. E. Marras
    Pages 273-290

  19. High-Throughput Production of Optimized Primers (Fimers) for Whole-Genome Direct Sequencing

    • Nikolai Polushin, Andrei Malykh, A. Michael Morocho, Alexei Slesarev, Sergei Kozyavkin
    Pages 291-304

  20. Nonenzymatic Template-Directed RNA Synthesis

    • Marcus Hey, Michael Göel
    Pages 305-318
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Editors and Affiliations

  • Rega Institute, Medicinal Chemistry Lab, Katholieke Universiteit Leuven, Leuven, Belgium

    Piet Herdewijn

Bibliographic Information

  • Book Title: Oligonucleotide Synthesis

  • Book Subtitle: Methods and Applications

  • Editors: Piet Herdewijn

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1385/1592598234

  • Publisher: Humana Totowa, NJ

  • eBook Packages: Springer Protocols

  • Copyright Information: Humana Press 2005

  • Hardcover ISBN: 978-1-58829-233-9Published: 01 September 2004

  • Softcover ISBN: 978-1-61737-441-8Published: 10 November 2010

  • eBook ISBN: 978-1-59259-823-6Published: 04 February 2008

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XVI, 436

  • Number of Illustrations: 142 b/w illustrations

  • Topics: Pharmacy

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